LINUM

Publications

Scientific articles

  1. Reina, F., Wigg, J. M. A., Dmitrieva, M., Vogler, B., Lefebvre, J., Rittscher, J., & Eggeling, C. (2022). TRAIT2D: A Software for Quantitative Analysis of Single Particle Diffusion Data. [version 2; peer review: 2 approved]. F1000Research 2022, 10:838(https://doi.org/10.12688/f1000research.54788.2)
  2. Sjoberg, H. T., Philippou, Y., Magnussen, A. L., Tullis, I. D. C., Bridges, E., Chatrian, A., Lefebvre, J., Tam, K. H., Murphy, E. A., Rittscher, J., Preise, D., Agemy, L., Yechezkel, T., Smart, S. C., Kinchesh, P., Gilchrist, S., Allen, D. P., Scheiblin, D. A., Lockett, S. J., ... Bryant, R. J. (2021). Tumour irradiation combined with vascular-targeted photodynamic therapy enhances antitumour effects in pre-clinical prostate cancer. British Journal of Cancer, 1-13. https://doi.org/10.1038/s41416-021-01450-6
  3. Lefebvre, J., Delafontaine-Martel, P., & Lesage, F. (2019). A Review of Intrinsic Optical Imaging Serial Blockface Histology (ICI-SBH) for Whole Rodent Brain Imaging. Photonics, 6(2), 66. https://doi.org/10.3390/photonics6020066
  4. Lefebvre, J., Delafontaine-Martel, P., Pouliot, P., Girouard, H., Descoteaux, M., & Lesage, F. (2018). Fully automated dual-resolution serial optical coherence tomography aimed at diffusion MRI validation in whole mouse brains. Neurophotonics, 5(4), 045004. https://doi.org/10.1117/1.NPh.5.4.045004
  5. Delafontaine-Martel, P., Lefebvre, J., Tardif, P.-L., Lévy, B. I., Pouliot, P., & Lesage, F. (2018). Whole brain vascular imaging in a mouse model of Alzheimer's disease with two-photon microscopy. Journal of Biomedical Optics, 23(07), 1. https://doi.org/10.1117/1.JBO.23.7.076501
  6. Castonguay, A., Lefebvre, J., Lesage, F., & Pouliot, P. (2018). Comparing three-dimensional serial optical coherence tomography histology to MRI imaging in the entire mouse brain. Journal of Biomedical Optics, 23(01), 1. https://doi.org/10.1117/1.JBO.23.1.016008
  7. Castonguay, A., Lefebvre, J., Pouliot, P., Avti, P., Moeini, M., & Lesage, F. (2017). Serial optical coherence scanning reveals an association between cardiac function and the heart architecture in the aging rodent heart. Biomedical Optics Express, 8(11), 5027. https://doi.org/10.1364/BOE.8.005027
  8. Lefebvre, J., Castonguay, A., Pouliot, P., Descoteaux, M., Lesage, F. (2017). Whole mouse brain imaging using optical coherence tomography: reconstruction, normalization, segmentation, and comparison with diffusion MRI. Neurophotonics, 4(4) 041501. https://doi.org/10.1117/1.NPh.4.4.041501
  9. Tardif, P.-L., Bertrand, M.-J., Abran, M., Castonguay, A., Lefebvre, J., Stähli, B., Merlet, N., Mihalache-Avram, T., Geoffroy, P., Mecteau, M., Busseuil, D., Ni, F., Abulrob, A., Rhéaume, É., L'Allier, P., Tardif, J.-C., & Lesage, F. (2016). Validating Intravascular Imaging with Serial Optical Coherence Tomography and Confocal Fluorescence Microscopy. International Journal of Molecular Sciences, 17(12), 2110. https://doi.org/10.3390/ijms17122110
  10. Gagnon, L., Sakad i, S., Lesage, F., Musacchia, J. J., Lefebvre, J., Fang, Q., Yucel, M. A., Evans, K. C., Mandeville, E. T., Cohen-Adad, J., Polimeni, J. R., Yaseen, M. A., Lo, E. H., Greve, D. N., Buxton, R. B., Dale, A. M., Devor, A., & Boas, D. A. (2015). Quantifying the Microvascular Origin of BOLD-fMRI from First Principles with Two-Photon Microscopy and an Oxygen-Sensitive Nanoprobe. Journal of Neuroscience, 35(8), 3663-3675. https://doi.org/10.1523/JNEUROSCI.3555-14.2015
  11. Sakadžić, S., Mandeville, E. T., Gagnon, L., Musacchia, J. J., Yaseen, M. A., Yucel, M. A., Lefebvre, J., Lesage, F., Dale, A. M., Eikermann-Haerter, K., Ayata, C., Srinivasan, V. J., Lo, E. H., Devor, A., & Boas, D. A. (2014). Large arteriolar component of oxygen delivery implies a safe margin of oxygen supply to cerebral tissue. Nature Communications, 5(1), 5734. https://doi.org/10.1038/ncomms6734
  12. Desjardins, M., Berti, R., Lefebvre, J., Dubeau, S., & Lesage, F. (2014). Aging-related differences in cerebral capillary blood flow in anesthetized rats. Neurobiology of Aging, 35(8), 1947-1955. https://doi.org/10.1016/j.neurobiolaging.2014.01.136
  13. Baraghis, E., Bolduc, V., Lefebvre, J., Srinivasan, V. J., Boudoux, C., Thorin, E., & Lesage, F. (2011). Measurement of cerebral microvascular compliance in a model of atherosclerosis with optical coherence tomography. Biomedical Optics Express, 2(11), 3079. https://doi.org/10.1364/BOE.2.003079

Conference papers

  1. Irgolitsch, Frans, Huppé-Marcoux, François, Lesage, Frédéric and Lefebvre, Joël (2024). Slice to volume registration using neural networks for serial optical coherence tomography of whole mouse brains. Computational Optical Imaging and Artificial Intelligence in Biomedical Sciences, 12857, 128570K-128570K-9. https://doi.org/10.1117/12.3002557
  2. Lefebvre, Joël, Pragassam, Alexia, Reynaud, Julien, Irgolitsch, Frans and Lesage, Frédéric (2024). Multiorientation mapping of white matter fiber microstructures in whole mouse brains using serial optical coherence tomography. Neural Imaging and Sensing 2024, 19. https://doi.org/10.1117/12.3002959
  3. Hawchar, Mohamad and Lefebvre, Joël (2023). Leveraging Self-attention Mechanism in Vision Transformers for Unsupervised Segmentation of Optical Coherence Microscopy White Matter Images. In International Workshop on Machine Learning in Medical Imaging (pp. 247-256). https://doi.org/10.1007/978-3-031-45673-2_25
  4. Lefebvre, Joël (2023). Exploring CNN-Based Self-Supervised Illumination Inhomogeneity Compensation for Serial Optical Coherence Tomography. 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), 00, 1-5. https://doi.org/10.1109/isbi53787.2023.10230803
  5. Abou-Hamdan, M., Cosenza, E., Miraux, S., Petit, L. and Lefebvre, J. (2023). Exploring the Allen Mouse Connectivity experiments with new neuroinformatic tools for neurophotonics, diffusion MRI and tractography applications. In SPIE Photonics West 2023. https://doi.org/10.1117/12.2649029 
  6. Lefebvre, J., Delafontaine-Martel, P., Lemieux, P., Descoteaux, M., Petit, L., & Lesage, F. (2021). Localization and imaging of white matter fiber crossings in whole mouse brains using diffusion MRI and serial blockface OCT. In Q. Luo, J. Ding, & L. Fu (Eds.), Optical Techniques in Neurosurgery, Neurophotonics, and Optogenetics (p. 56). SPIE. https://doi.org/10.1117/12.2577648
  7. Lefebvre, J., Javer, A., Dmitrieva, M., Rittscher, J., Lewkow, B., Allgeyer, E., Sirinakis, G., & Johnston, D. St. (2020). Single-Molecule Localization Microscopy Reconstruction Using Noise2Noise for Super-Resolution Imaging of Actin Filaments. 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), 1596-1599. https://doi.org/10.1109/ISBI45749.2020.9098713
  8. Dmitrieva, M., Lefebvre, J., delas Penas, K., Zenner, H. L., Richens, J., St Johnston, D., & Rittscher, J. (2020). Short Trajectory Segmentation with 1D UNET Framework: Application to Secretory Vesicle Dynamics. 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), 891-894. https://doi.org/10.1109/ISBI45749.2020.9098426
  9. delas Penas, K., Dmitrieva, M., Lefebvre, J., Zenner, H., Allgeyer, E., Booth, M., St Johnston, D., & Rittscher, J. (2020). Extracting Axial Depth and Trajectory Trend Using Astigmatism, Gaussian Fitting, and CNNs for Protein Tracking. 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), 1634-1637. https://doi.org/10.1109/ISBI45749.2020.9098364
  10. Lefebvre, J., Castonguay, A., & Lesage, F. (2018). Imaging whole mouse brains with a dual resolution serial swept-source optical coherence tomography scanner. In Q. Luo & J. Ding (Eds.), Neural Imaging and Sensing 2018 (p. 12). SPIE. https://doi.org/10.1117/12.2288521
  11. Delafontaine-Martel, P., Lesage, F., Damseh, R., Lefebvre, J., Castonguay, A., & Tardif, P.-L. (2018). Large scale serial two-photon microscopy to investigate local vascular changes in whole rodent brain models of Alzheimer's disease. In A. Periasamy, P. T. So, X. S. Xie, & K. König (Eds.), Multiphoton Microscopy in the Biomedical Sciences XVIII (p. 92). SPIE. https://doi.org/10.1117/12.2290060
  12. Lefebvre, J., Castonguay, A., & Lesage, F. (2017). White matter segmentation by estimating tissue optical attenuation from volumetric OCT massive histology of whole rodent brains. Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIV, 10070, 1007012. https://doi.org/10.1117/12.2251173
  13. Lesage, F., Castonguay, A., Tardif, P. L., Lefebvre, J., & Li, B. (2015). Investigating the impact of blood pressure increase to the brain using high resolution serial histology and image processing. In M. Papadakis, V. K. Goyal, & D. Van De Ville (Eds.), Wavelets and Sparsity XVI (pp. 95970M). https://doi. org/10.1117/12.2189110
  14. Sakadžić, S., Mandeville, E. T., Gagnon, L., Musacchia, J. J., Yaseen, M. A., Yucel, M. A., Lefebvre, J., Lesage, F., Dale, A. M., Eikermann-Haerter, K., Ayata, C., Srinivasan, V. J., Lo, E. H., Devor, A., & Boas, D. A. (2014). Oxygen Distribution in Cortical Microvasculature Reveals a Novel Mechanism for Maintaining a Safe Tissue Oxygenation. Biomedical Optics 2014, BW1A.2. https://doi.org/10.1364/BIOMED.2014.BW1A.2
  15. Sakadžić, S., Mandeville, E. T., Gagnon, L., Musacchia, J. J., Yaseen, M. A., Yucel, M. A., Lefebvre, J., Lesage, F., Dale, A. M., Eikermann-Haerter, K., Ayata, C., Srinivasan, V. J., Lo, E. H., Devor, A., & Boas, D. A. (2014). High-Resolution Optical Microscopy Imaging of Cortical Oxygen Delivery and Consumption. CLEO: 2014, AF2B.3. https://doi.org/10.1364/CLEO_AT.2014.AF2B.3
  16. Gagnon, L., Sakadžić, S., Lesage, F., Musacchia, J. J., Lefebvre, J., Fang, Q., Yücel, M. A., Evans, K. C., Mandeville, E. T., Cohen-Adad, J., Polimeni, J. R., Yaseen, M. A., Lo, E. H., Greve, D. N., Buxton, R. B., Dale, A. M., Devor, A., & Boas, D. A. (2014). Underpinning the microvascular origin of BOLD-fMRI with two-photon microscopy. Biomedical Optics 2014, BT4A.1. https://doi.org/10.1364/BIOMED.2014.BT4A.1
  17. Gagnon, L., Sakadžić, S., Lesage, F., Musacchia, J. J., Lefebvre, J., Fang, Q., Yucel, M. A., Evans, K. C., Mandeville, E. T., Cohen-Adad, J., Polimeni, J. R., Yaseen, M. A., Lo, E. H., Greve, D., Buxton, R., Dale, A. M., Devor, A., & Boas, D. A. (2014). Folded cortical orientation influences the amplitude of BOLD-fMRI: evidence from simulations and experimental data. Proc. Intl. Soc. Mag. Reson. Med. 22, 3084.
  18. Desjardins, M., Berti, R., Lefebvre, J., Dubeau, S., & Lesage, F. (2014). Microscopic Dynamics of Cerebral Capillary Blood Flow in Aged Anesthetized Rats. Biomedical Optics 2014, BT3A.3. https://doi.org/10.1364/BIOMED.2014.BT3A.3

Preprints

  1. N.A.

Presentations

  1. Comtois, E., Lefebvre, J., Meurs, M.-J. (2024). Characterization and analysis of the urban arboreal environment: a digital twin by drone photographic survey. Rendez-vous arboricole SIAQ, November 2024. Remote (Laval, Canada). [Oral].
  2. Hawchar, M., Poirier, C., Lefebvre, J. (2024). Dual Resolution S-OCT and dMRI Dataset of Whole Mouse Brains. Quebec Connectome Conference, October 2024. In attendance (Orford, Canada). [Poster]
  3. Huppé-Marcoux, F., Hawchard, M., Irgolitsch, F., Carignan, G., Lefebvre, J. (2024). Developing a Web-based Serial Blockface Histology Assistant. Quebec Connectome Conference, October 2024. In attendance (Orford, Canada). [Poster]
  4. Irgolitsch, F., Lefebvre, J., Lesage, F. (2024). Mesoscale imaging and analysis of the whole mouse brain using Light Sheet Fluorescence Microscopy. Quebec Connectome Conference, October 2024. In attendance (Orford, Canada). [Oral].
  5. Poirier, C., Lefebvre, J., Descoteaux, M. (2024). Extracting three-dimensional orientations from serial optical coherence tomography of whole mouse brains. Quebec Connectome Conference, October 2024. In attendance (Orford, Canada). [Oral]
  6. St-Denis, A., Meurs, M.-J., Lefebvre, J., Nicol, M., Comtois, E., Assouane, S. (2024) SylvCiT and an overview of the ArbrenVil Chair's informatics projects. Presentation to Chaire ArbrenVil partners, August 2024. Remote (Montreal, Canada). [Oral].
  7. Comtois, E., Lefebvre, J., Meurs, M.-J. (2024). Mapping and characterization of urban trees by drone photographic survey. 91st Acfas Congress, May 2024. Pre-recorded (Ottawa, Canada). [Oral].
  8. Abou-Hamdan, M., Cosenza, E., Miraux, S., Petit, L. and Lefebvre, J. (2023). Exploring the Allen Mouse Connectivity experiments with new neuroinformatic tools for neurophotonics, diffusion MRI and tractography applications. SPIE Photonics West 2023. In attendance (San Francisco, USA) [Oral]
  9. Lemieux, P., Rambaud, B., Carreno, S., Lefebvre, J. (2022). Detecting the 3D morphology of cell cytonemes using skeletonization. IEEE 19th International Symposium on Biomedical Imaging (ISBI). Remote (Calcutta, India) [Oral]
  10. de Oliveira-Sicard, G., Massi, F., Tu, J., Descoteaux, M., Lefebvre, J. (2021). Cell-level detection of 3D white matter orientation for tractography based on light sheet microscopy. CERMO-FC Symposium. In attendance (Montreal, Canada). [Poster]

Theses

  1. Pouliot, Philippe (2024). "Segmentation and analysis of 3D microscopic data for cytonemal cell morphology". Dissertation. Montréal (Québec, Canada), Université du Québec à Montréal, Maîtrise en informatique. https://archipel.uqam.ca/18120/
  2. Faubert Laurin, Maxime (2023). "Automatic tree identification from photos". Dissertation. Montréal (Québec, Canada), Université du Québec à Montréal, Maîtrise en informatique. https://archipel.uqam.ca/18260/
  3. Hawchar, Mohamad (2023). "Self-supervised learning with vision transformers for unsupervised segmentation of optical coherence microscopy white matter images" Thesis. Montréal (Québec, Canada), Université du Québec à Montréal, Master of Computer Science. https://archipel.uqam.ca/17336/
  4. Lefebvre, J. (2018). Multimodal and multiresolution neuroimaging of mouse brains combining serial histology by optical coherence tomography and diffusion MRI [Ph.D., École Polytechnique de Montréal]. https://publications.polymtl.ca/3273/
  5. Lefebvre, J. (2014). Development of tools for vectorization of angiographies obtained by 2-photon microscopy in the context of brain aging [Masters, École Polytechnique de Montréal]. https://publications.polymtl.ca/1515/